But aides to President Obama clearly were intent on keeping her in the fold, at least with flattering messages. After she injured her elbow in a fall, David Axelrod, the president's senior adviser, sent her a message with the subject line "So sorry!" expressing hope that she get better soon. "You are an all-star player, and we need you for the long run!" he wrote.
Still, the suspicion ran deep. Before Mr. Axelrod sent her the message, he had to ask her aides for her address, and the aides checked with her first about whether it was O.K. to give to him. They similarly asked whether it was all right to give her address to Rahm Emanuel, then the White House chief of staff.
Her policy priorities come through in the messages as well. In July 2009, when an aide forwarded Mrs. Clinton a message about treatment of gays and lesbians in Iraq, both before and after the reign of Saddam Hussein, she wrote back quickly: "So sad and terrible. We should ask Chris Hill," the American ambassador, "to raise w govt."
Read MoreClinton vows wage gap attack
Mrs. Clinton's husband, former President Bill Clinton, is known for not using email, but he makes cameo appearances in messages from others. At times, it seems, the Clintons communicated with each other through their aides.
In May 2009, Doug Band, the former president's adviser, wrote to Cheryl Mills, the secretary's chief of staff, to inform her that Mr. Clinton had accepted the role of United Nations special envoy to Haiti and that the news had begun to leak. "WJC said he was going to call HRC but hasn't had time," Mr. Band wrote, using initials for the couple. Ms. Mills forwarded the email to another aide and said, "You need to walk this to HRC if she is not gone."
While an ostensibly nonpartisan figure as secretary, Mrs. Clinton clearly still worried about retiring her $23 million campaign debt from 2008. "Thank you so very much!!!" her chief of protocol, Capricia Marshall, wrote to Paul Begala, a longtime Clinton friend and Democratic strategist, in April 2009. "We raised 500K from the email contest!! You are all amazing — the world adores you!" She added, "You put a serious hole in HRC debt!"
Mr. Begala responded by asking for talking points before he went on CNN to rate Mrs. Clinton's early performance. Ms. Marshall referred him to several State Department aides. After his appearance, Mr. Begala emailed back: "I gave Sec. Clinton an A+ in our dopey CNN report card last night." Ms. Mills forwarded that to Mrs. Clinton with an "FYI."